-
Notifications
You must be signed in to change notification settings - Fork 0
/
aquamonitor.py
430 lines (322 loc) · 13 KB
/
aquamonitor.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
__author__ = 'Roar Brenden'
import requests
from xml.dom import minidom
import json
import configparser
import pyexpat
import time
import datetime
import getpass
import pandas as pd
from pandas.io.json import json_normalize
host = 'http://www.aquamonitor.no/'
aqua_site = 'AquaServices'
archive_site = 'AquaServices'
cache_site = 'AquaCache'
def requestService(url, params):
response = requests.post(url, params)
try:
return minidom.parseString(response.text)
except pyexpat.ExpatError as e:
print("URL: " + url)
print("PARAMS:" + ''.join('{}={} '.format(key, val) for key, val in params.items()))
print("RESPONSE:" + response.text)
raise e
def login(username=None, password=None):
if username is None:
config = configparser.RawConfigParser()
try:
config.read(".auth")
username = config.get("Auth", "username")
password = config.get("Auth", "password")
except Exception as ex:
raise Exception("Couldn't read username/password in file .auth")
loginurl = aqua_site + '/login'
loginparams = {'username': username, 'password': password}
userdict = postJson(None, loginurl, loginparams)
usertype = userdict["Usertype"]
if not usertype == 'NoUser':
token = userdict["Token"]
else:
token = None
return token
def jhub_login(username=None, password=None):
if username is None:
# Get credentials
print('Please enter your Aquamonitor username and password:')
username = getpass.getpass(prompt='Username: ')
password = getpass.getpass(prompt='Password: ')
loginurl = aqua_site + '/login'
loginparams = {'username': username, 'password': password}
userdict = postJson(None, loginurl, loginparams)
usertype = userdict["Usertype"]
if not usertype == 'NoUser':
token = userdict["Token"]
print('Log-in successful.')
else:
token = None
print('Log-in failed.')
return token
def get(token: str, site: str, path: str, stream: bool = False):
return requests.get(host + site + path, cookies=dict(aqua_key=token), stream=stream)
def reportJsonError(response):
message = "AquaMonitor failed with status: " + response.reason + " and message:"
if response.text is not None:
try:
message = message + "\n\n" + json.loads(response.text).get("Message")
except:
message = message + "\nDidn't send JSON."
raise Exception(message)
def getJson(token, path):
response = requests.get(host + path, cookies = dict(aqua_key=token))
if response.status_code == 200:
return json.loads(response.text)
else:
reportJsonError(response)
def postJson(token, path, inJson):
response = requests.post(host + path, json=inJson, cookies=dict(aqua_key=token))
if response.status_code == 200:
return json.loads(response.text)
else:
reportJsonError(response)
def putJson(token, path, inJson):
response = requests.put(host + path, json=inJson, cookies=dict(aqua_key=token))
return json.loads(response.text)
def deleteJson(token, path):
response = requests.delete(host + path, cookies=dict(aqua_key=token))
return json.loads(response.text)
def getProject(token, projectId):
projectsurl = 'AquaServices/api/projects/'+ str(projectId)
return getJson(token, projectsurl)
def getStations(token, projectId):
stationsurl = 'AquaServices/api/projects/' + str(projectId) + '/stations/'
return getJson(token, stationsurl)
def getArchive(token, id):
path = archive_site + '/files/archive/' + id
return getJson(token, path)
def createDatafile(token, data):
path = archive_site + '/files/datafile/'
return postJson(token, path, data)
def deleteArchive(token, id):
path = archive_site + '/files/archive/' + id
return deleteJson(token, path)
def downloadFile(token, url, path):
resp = get(token, "", url)
with open(path, 'wb') as fd:
for chunk in resp.iter_content(chunk_size=256):
fd.write(chunk)
def downloadArchive(token, id, file, path):
downloadFile(token, archive_site + "/files/archive/" + id + '/' + file, path)
class Query:
key = None
table = None
result = None
def __init__(self, where, token):
self.token = token
self.where = where
def map(self, table=None):
if self.token is None:
self.token = login()
self.table = table
if self.key is None:
self.createQuery()
if self.key is not None:
self.waitQuery()
if self.result.get("ErrorMessage") is None:
if table is None:
return self.result["CurrentStationIds"]
else:
return self.result["Items"]
else:
raise Exception("Query ended with an error: " + self.result["ErrorMessage"])
def makeArchive(self, fileformat, filename):
if self.token is None:
self.token = login()
if self.key is None:
self.createQuery()
if not self.key is None:
self.waitQuery()
if self.result.get("ErrorMessage") is None:
return Archive(fileformat, filename,
token=self.token,
stations=self.result["CurrentStationIds"],
where=self.where)
else:
raise Exception("Query ended with an error: " + self.result["ErrorMessage"])
def waitQuery(self):
resp = getJson(self.token, cache_site + "/query/" + self.key)
if not resp.get("Result") is None:
while not resp["Result"]["Ready"]:
time.sleep(1)
resp = getJson(self.token, cache_site + "/query/" + self.key)
if self.table is None:
self.result = resp["Result"]
else:
resp = getJson(self.token, cache_site + "/query/" + self.key + "/" + self.table)
if not resp.get("Ready") is None:
while not resp["Ready"]:
time.sleep(1)
resp = getJson(self.token, cache_site + "/query/" + self.key + "/" + self.table)
self.result = resp
else:
raise Exception("Query didn't respond properly for table request: " + self.table)
else:
raise Exception("Query didn't respond properly.")
def createQuery(self):
query = {}
if self.table is not None:
query["From"] = [{"Table":self.table}]
if self.where is not None:
query["Where"] = self.where
resp = postJson(self.token, cache_site + "/query/", query)
if resp.get("Key") is None:
raise Exception("Couldn't create query. Response: " + str(resp))
else:
self.key = resp["Key"]
class Archive:
id = None
expires = None
token = None
def __init__(self, *args, **kwargs):
if args.__len__() == 1:
self.id = args[0]
elif args.__len__() == 2:
self.fileformat = args[0]
self.filename = args[1]
self.token = kwargs.get("token")
self.stations = kwargs.get("stations")
self.where = kwargs.get("where")
def download(self, path):
if self.id is None:
self.createArchive()
if not self.id is None:
resp = getArchive(self.token, self.id)
while resp.get("Archived") is None:
time.sleep(5)
resp = getArchive(self.token, self.id)
for file in resp["Files"]:
downloadArchive(self.token, self.id, file["FileName"], path + file["FileName"])
else:
print("Couldn't create archive.")
def createArchive(self):
if self.expires is None:
self.expires = datetime.date.today() + datetime.timedelta(days=1)
if self.token is None:
self.token = login()
if self.fileformat == "excel":
content_type = "application/vnd.ms-excel"
elif self.fileformat == "csv":
content_type = "text/csv"
else:
content_type = "text/plain"
archive = {
"Expires": self.expires.strftime('%Y.%m.%d'),
"Title": "QueryExample",
"Files": [{
"Filename": self.filename,
"ContentType": content_type}],
"Definition": {
"Format": self.fileformat,
"StationIds": self.stations,
"DataWhere": self.where
}
}
resp = createDatafile(self.token, archive)
if not resp.get("Id") is None:
self.id = resp["Id"]
def queryGraph(token, document):
""" Interface to GraphQL API.
"""
resp = requests.post(host + aqua_site + "lab/graphql", json=document,
cookies=dict(aqua_key=token))
print(resp)
return resp.json()['data']
def get_labware_projects(token, proj_code):
""" Get all Labware 'projects' for the specified NIVA project.
Args:
token: Obj. Valid authentication token for AM
proj_code: Str. NIVA project code e.g. '190091;3' for the 1000 Lakes
Returns:
Dataframe
"""
proj_code = str(proj_code)
resp = queryGraph(token, {
"query": "query getProjects($nr: String) {projects(projectNr: $nr){name,status,closed}}",
"variables": {
"nr": proj_code
}
})
return json_normalize(resp['projects'])
def get_labware_project_samples(token, proj_list):
""" Get all Labware samples for the specified list of Labware projects.
Args:
token: Obj. Valid authentication token for AM
proj_list: Iterable. List of Labware project names
Returns:
Dataframe
"""
# Containers for data
df_list = []
lw_id_list = []
id_list = []
name_list = []
type_list = []
for proj in proj_list:
# Get sample data
resp = queryGraph(token, {
"query": "query getSamples($name: String) {samples(projectName: $name){sampleNumber,textID,"
"projectStationId,status,sampledDate,sampleDepthUpper,sampleDepthLower}}",
"variables": {
"name": proj
}
})
resp = json_normalize(resp['samples'])
df_list.append(resp)
for stn_id in resp['projectStationId'].unique():
try:
stn_data = getJson(token, aqua_site + f"api/stations/{stn_id}")
lw_id_list.append(stn_id)
id_list.append(stn_data['Id'])
name_list.append(stn_data['Name'])
type_list.append(stn_data['Type']['_Text'])
except:
#print(f'Station with projectStationId {stn_id} is not in Aquamonitor.')
pass
samp_df = pd.concat(df_list, axis='rows', sort=True)
stn_df = pd.DataFrame({'projectStationId':lw_id_list,
'station_id': id_list,
'station_name': name_list,
'station_type': type_list,
})
stn_df.drop_duplicates(inplace=True)
samp_df = pd.merge(samp_df, stn_df,
how='left',
on='projectStationId',
)
samp_df = samp_df[['sampleNumber', 'textID', 'projectStationId', 'status', 'sampledDate',
'sampleDepthUpper', 'sampleDepthLower', 'station_id', 'station_name',
'station_type']]
return samp_df
def get_labware_sample_results(token, samp_list):
""" Get all Labware results for the specified list of samples.
Args:
token: Obj. Valid authentication token for AM
samp_list: Iterable. List of Labware sampleNumbers
Returns:
Dataframe
"""
df_list = []
for samp in samp_list:
assert isinstance(samp, int), 'sampleNumbers must be integers.'
resp = queryGraph(token, {
"query": "query getResults($nr: Int) {results(sampleNumber: $nr){name,units,analysis,accreditedId,entryQualifier,"
"numericEntry,mu,loq,status}}",
"variables": {
"nr": samp
}
})
res_df = json_normalize(resp['results'])
res_df['sample_id'] = samp
df_list.append(res_df)
res_df = pd.concat(df_list, axis='rows', sort=True)
return res_df